Author response: Mechanism of allosteric regulation of β2-adrenergic receptor by cholesterol

Characterization of Lipid–Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation

“…393 Cholesterol is also known to alter the dynamics of GPCRs. 411 Its binding has been shown to alter the conformational dynamics of β 1 AR 412 and β 2 AR 413 A μs-AA simulation showed that cholesterol binding at the helical interface limits the conformational variability of β 2 AR, 413 thus establishing an allosteric role for cholesterol in modulation of the protein. Similarly, a short MD simulation of a peptide representing one of the transmembrane helices of 5-HT 2A R demonstrated that the lipid bilayer with the help of a few water molecules can stabilize the helical elements, even in the presence of helix-disrupting prolines.…”

“…419 In a later study, a pathway for cholesterol access to the A 2A R ligand binding pocket was discovered, indicating a distinct mechanism of cholesterol action by directly modulating the orthosteric ligand binding site. 748 Apart from AA simulations, two CG simulations have elucidated how cholesterol molecules may facilitate ligand binding in 5-HT 1A R 415 and how agonists affect cholesterol binding to β2AR and A 2A R. 420 Additionally, long-timescale AA simulations have shown the influence of cholesterol on the conformational dynamics of several GPCRs, including β 1 AR, 412 β 2 AR, 413 5-HT 1A R 416 and 5-HT 2A R. 390,417 As an example, μs simulations unveiled reduced conformational variability of β 2 AR caused by cholesterol binding (Figure 40C), suggesting an allosteric modulation of β 2 AR. 413 Long-timescale simulations have also characterized a special modulatory effect of cholesterol on stabilizing the secondary structure of an amphipathic juxtamembrane helix in CB 1 , 749 a class A GPCR, and mGluR2, 750 a class C GPCR.…”

“…748 Apart from AA simulations, two CG simulations have elucidated how cholesterol molecules may facilitate ligand binding in 5-HT 1A R 415 and how agonists affect cholesterol binding to β2AR and A 2A R. 420 Additionally, long-timescale AA simulations have shown the influence of cholesterol on the conformational dynamics of several GPCRs, including β 1 AR, 412 β 2 AR, 413 5-HT 1A R 416 and 5-HT 2A R. 390,417 As an example, μs simulations unveiled reduced conformational variability of β 2 AR caused by cholesterol binding (Figure 40C), suggesting an allosteric modulation of β 2 AR. 413 Long-timescale simulations have also characterized a special modulatory effect of cholesterol on stabilizing the secondary structure of an amphipathic juxtamembrane helix in CB 1 , 749 a class A GPCR, and mGluR2, 750 a class C GPCR. The observed stabilization was attributed either to a cooperation of cholesterol binding near the CCM site and palmitoylation of a cysteine residue, 749 or to a combination of direct interaction and indirect membrane thickening effects of cholesterol.…”

The good, the bad and the user in soft matter simulations

“…Sampling issues in MD have recently been reviewed by Grossfield and Zuckerman [21] and they are discussed in this issue in the article of Pomes et al [22]. In addition to algorithms and protocols, system preparation should be paid due attention as has been pointed out by Manna et al [23]. As a side note, in the context of numerical analysis, it has been pointed out that it is not clear at all why MD even works!…”